Structural Molecular Biology

Objectives:

The course aims to give students knowledge regarding the relationship between biomacromolecules structure and their function, as well as skills applicable towards solving relevant problems. Students will learn about methodologies to determine structures, how to analyze them, and understand their biological and biomolecular properties. There will be an emphasize on how several biomacromolecules assemble into functional assemblies and how these give rise to properties important for cells or the organisms. Developing a student’s ability to solve problems within structural biology at an advanced level is an important goal for the course.

Content:

The primary biomolecular focus of the course will be proteins. Other biomolecules and assemblies of biomolecule will generally only be discussed in connection with their relationship to proteins. Topics that will be covered include how amino acids are assembled into primary, secondary, tertiary and higher order structures and complexes, and how functional protein properties then emerge. The course will offer introductions into relevant methodology, how protein structures are determined and explored both experimentally and by computational techniques. It will assume prior knowledge in fundamental protein chemistry, some cell biology and biochemistry, as well as the application of multiple sequence alignments. The course will build on concepts that has already been introduced earlier, including protein folding, allostery, catalysis and enzymology, ligand and effector binding, post-translational modifications, and signaling. An important aspect of the course will be how all these phenomena regulates, and is regulated by, protein function. The course will also discuss the structural and biochemical basis of molecular signaling, as well as enzyme function from a structural, kinetic and thermodynamical point of view. Protein evolution from as sequence and structural perspective will be covered, as will diverse molecular topics within protein-ligand interaction, protein folding, and macromolecular assembly. Methodologies, especially those related to determining and analyzing structure, folding and binding behavior, will be introduced and discussed with the aim of improving student ability to plan how to approach and solve practical and theoretical problems in structural and molecular biology.

On completion of the course the student should have the following learning outcomes defined in terms of knowledge, skills and general competence:

Knowledge

The student can provide detailed explanations about

• forces and effects that leads to the formation of protein structure, and the different levels of protein structure, from the amino-acid level to larger, quaternary complexes
• how a protein uses its structural organization to achieve traits that do not occur in its individual components
• protein classification by structure and function
• how these properties underpin function at the molecular level in a living organism
• how enzymes attain their unique properties
• how these protein functions are controlled by modification, localization and effector interactions
• Mass Spectrometry Cryo-EM, NMR, X-ray diffraction and computational techniques for determining structure at different levels of organization.
• In addition to the above, CD, fluorescence, and other relevant methodology to study protein fold, stability, binding behavior, and function
• how evolution act on protein primary sequence, structure and function

Skills

The student is able to

• analyze structure-function relationships when presented with biological and structural information
• explain (orally and in writing) how the topics outlined above acts together in cell processes such as signal transduction, endo / exocytosis, cell motility and gene regulation
• choose the right methodology in order to answer simple (and possibly also difficult) questions linked to a given macromolecular problem
• use information derived from methodologies relevant for the course to solve protein structure-function problems
• orient themselves in the spatial- and temporal scale that is associated with macromolecular understanding (that is, Ångstrøm to nanometers, ps-ms)
• solve theoretical tasks related to the topics discussed in the course
• use PyMol, a program for working with protein structures, at a novice level
• work in a group to produce a (compulsory) written assignment about aMOL310">relevant topic for the course that the group chooses from a set menu. The group must also provide constructive assessment and feedback to the assignments of other groups. The assignments must maintain a good level with respect to student insight, clarity of presentation and proper use of terminology.

General competence

The student has

• the ability to place concepts discussed in the courseMOL310">into a wider biological and chemical context, and moreover, reach their own conclusions independently of existing material
• solve problems within structural biology at an advanced level
• understood how particular protein achieves its specific and unique characteristics
• the ability to convey qualitative and quantitative aspects of structural molecular biology, by oral and written means, to both specialists and non-specialists
• the ability to navigate, understand and make use of protein classification, content in The Protein Databank, and UniProt and protein classification for the purpose of scientific communication (i.e., the written assignment)
• use scientific sources and tools to pursue and solve problems related to structural biology

Spring.

This course has a limited capacity, enrolment is based on application. The application deadline is Wednesday in week 2 for the spring semester. Please see this page for more information. You will receive confirmation of whether you received a seat in Studentweb no later than Monday the week after the deadline.

It is compulsory to attend the first lecture/orientation meeting, or you risk losing your seat. If you are unable to attend the first lecture, you must contact the Study Section (studie.bio@uib.no). The time of the first lecture/orientation meeting can be found in the schedule on the course website or on Mitt UiB.